Showing : DESEQ2 • reset
1
vote
3
replies
104
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 19 hours ago by 66k • written 1 day ago by ▴ 720
0
votes
6
replies
558
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
4 days ago • updated 22 hours ago Ken C • 0
2
votes
4
replies
187
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 21 hours ago by 42k • written 3 days ago by • 0
4
votes
9
replies
287
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 5 days ago by ★ 4.1k • written 6 days ago by • 0
0
votes
3
replies
136
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 6 days ago by 42k • written 6 days ago by • 0
0
votes
1
reply
106
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 6 days ago by 42k • written 7 days ago by • 0
0
votes
8
replies
530
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 6 days ago by ▴ 30 • written 7 days ago by • 0
1
vote
2
replies
259
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
7 days ago • updated 4 days ago BioinfGuru ▴ 30
0
votes
1
reply
187
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
0
votes
1
reply
116
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 12 days ago by ★ 4.1k • written 12 days ago by • 0
2
votes
7
replies
424
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
13 days ago • updated 10 days ago sajadahmad41454 • 0
1
vote
1
reply
195
views
Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by 42k • written 17 days ago by ▴ 10
0
votes
6
replies
307
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 17 days ago by ★ 1.4k • written 18 days ago by ▴ 130
2
votes
3
replies
264
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
0
votes
2
replies
175
views
DESeq2 v1.35.0
DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
0
votes
2
replies
217
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago kcarey • 0
0
votes
3
replies
230
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 days ago by ★ 4.1k • written 19 days ago by • 0
1
vote
3
replies
307
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 13 days ago by ★ 4.1k • written 19 days ago by • 0
0
votes
3
replies
305
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 days ago by 42k • written 20 days ago by • 0
1
vote
1
reply
161
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
0
votes
2
replies
172
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
21 days ago • updated 18 days ago Aurora • 0
0
votes
1
reply
140
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
0
votes
1
reply
141
views
putting my own expression data in deseq2
DESeq2
updated 21 days ago by ★ 4.1k • written 21 days ago by • 0
3
votes
3
replies
275
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 22 days ago by ★ 4.1k • written 22 days ago by ▴ 10
0
votes
2
replies
229
views
PCA plot suggestions
DESeq2 PCAtools
updated 24 days ago by 42k • written 26 days ago by • 0
1
vote
3
replies
257
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 25 days ago by 42k • written 25 days ago by • 0
2
votes
9
replies
430
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 25 days ago by 66k • written 26 days ago by • 0
0
votes
1
reply
167
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 26 days ago by 42k • written 26 days ago by • 0
1
vote
3
replies
240
views
Different Shrunk Log2FC according with reference
DESeq2
updated 27 days ago by 42k • written 27 days ago by ▴ 20
1
vote
4
replies
362
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
27 days ago • updated 25 days ago winwater0928 • 0
3
votes
1
reply
329
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 27 days ago by 42k • written 27 days ago by ▴ 40
0
votes
8
replies
398
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 26 days ago by ★ 1.4k • written 27 days ago by • 0
3
votes
3
replies
254
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 28 days ago by 42k • written 28 days ago by • 0
0
votes
1
reply
158
views
rlog transformation
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
votes
1
reply
130
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
1
vote
2
replies
756
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 25 days ago Patadù ▴ 10
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
votes
1
reply
169
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
0
votes
4
replies
272
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago lonn • 0
0
votes
3
replies
233
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 20
1
vote
2
replies
266
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 4 weeks ago Weiqian ▴ 10
0
votes
4
replies
293
views
DEG with low counts
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
0
votes
1
reply
151
views
Deseq2 Rlog transformation
DESeq2
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
1
vote
2
replies
216
views
Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago hemantcnaik • 0
0
votes
1
reply
154
views
Bioinformatics student
Des DESeq2
updated 5 weeks ago by • 0 • written 5 weeks ago by • 0
0
votes
1
reply
202
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago Shefali • 0
0
votes
2
replies
248
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 weeks ago by 42k • written 6 weeks ago by ▴ 30
0
votes
1
reply
193
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
votes
2
replies
267
views
Regressing out batch effects
DESeq2
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
0
votes
2
replies
184
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 6 weeks ago by 66k • written 6 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: ChAMP installation issue by Tahirah • 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by James W. MacDonald 66k
Yes, you can use `limma`.
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Awards • All
Scholar to Mike Smith ★ 6.5k
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to bas_work ▴ 30
Popular Question to landenshanie ▴ 40
Locations • All
EMBL Heidelberg, just now
Slovakia, 1 minute ago
Germany, 2 minutes ago
United States, 2 minutes ago
Belgium, 7 minutes ago
Traffic: 766 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6